Separation of reduced and permethylated oligosaccharides by gas chromatography can be facilitated by the use of a fused silica capillary column coated with methyl silicon. The presence of N-acetylhexosamines in oligosaccharides increases their retention time and interferes with efficient GC separation. Transamidation of hexosamines by trifluoroacetolysis followed by reduction, removal of O-trifluoroacetyl groups and permethylation, dramatically reduces the retention time of hexosamine-containing oligosaccharides and permits separation of oligosaccharides containing up to six monosaccharide units, regardless of how many of these are hexosamines. The mass spectra of permethylated oligosaccharides with N-trifluoroacetylated amino sugars show unexpectedly high abundances of mass ions containing the N-trifluoroacetyl group. As many of these ions are large, they provide useful information regarding oligosaccharide structure.